R4RNA: An R package for RNA visualization and analysis

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A package for RNA basepair analysis, including the visualization of basepairs as arc diagrams for easy comparison and annotation of sequence and structure. Arc diagrams can additionally be projected onto multiple sequence alignments to assess basepair conservation and covariation, with numerical methods for computing statistics for each.

Author
Daniel Lai, Irmtraud Meyer <irmtraud.meyer@cantab.net>
Date of publication
None
Maintainer
Daniel Lai <jujubix@cs.ubc.ca>
License
GPL-3
Version
1.2.0
URLs

View on Bioconductor

Man pages

alignmentStatistics
Compute statistics for a multiple sequence alignments
as.helix
Coerce to a Helix Data Frame
basepairFrequency
Calculates the frequency of each basepair
blankPlot
Create a blank plotting canvas
colourHelices
Assign colours to helices
expandCollapseHelix
Expand or collapse helices to and from basepairs
helix
Helices predicted by TRANSAT with p-values
logicalHelix
Logical filters of helix by type
logseq
Log base 10 sequence, floor and ceiling
plotCovariance
Plot nucleotide sequence coloured by covariance
plotHelix
Plots helices in arc diagram
R4RNA-package
An R package for RNA visualization and analysis
readStructure
Read secondary structure file
structureMismatchScore
Scores how a basepair structure fits a sequence
unknottedGroups
Partition basepairs into unknotted groups
viennaToHelix
Convert helix structures to and from other formats
writeHelix
Write out a helix data frame into a text file

Files in this package

R4RNA/DESCRIPTION
R4RNA/NAMESPACE
R4RNA/NEWS
R4RNA/R
R4RNA/R/io.R
R4RNA/R/misc.R
R4RNA/R/plot.R
R4RNA/R/stats.R
R4RNA/build
R4RNA/build/vignette.rds
R4RNA/data
R4RNA/data/helix.RData
R4RNA/inst
R4RNA/inst/CITATION
R4RNA/inst/doc
R4RNA/inst/doc/R4RNA.R
R4RNA/inst/doc/R4RNA.Rnw
R4RNA/inst/doc/R4RNA.pdf
R4RNA/inst/extdata
R4RNA/inst/extdata/bpseq.txt
R4RNA/inst/extdata/connect.txt
R4RNA/inst/extdata/fasta.txt
R4RNA/inst/extdata/helix.txt
R4RNA/inst/extdata/vienna.txt
R4RNA/man
R4RNA/man/R4RNA-package.Rd
R4RNA/man/alignmentStatistics.Rd
R4RNA/man/as.helix.Rd
R4RNA/man/basepairFrequency.Rd
R4RNA/man/blankPlot.Rd
R4RNA/man/colourHelices.Rd
R4RNA/man/expandCollapseHelix.Rd
R4RNA/man/helix.Rd
R4RNA/man/logicalHelix.Rd
R4RNA/man/logseq.Rd
R4RNA/man/plotCovariance.Rd
R4RNA/man/plotHelix.Rd
R4RNA/man/readStructure.Rd
R4RNA/man/structureMismatchScore.Rd
R4RNA/man/unknottedGroups.Rd
R4RNA/man/viennaToHelix.Rd
R4RNA/man/writeHelix.Rd
R4RNA/vignettes
R4RNA/vignettes/R4RNA.Rnw